RESULTS SUMMARY - Based on abricate results
|
SAMPLEID
|
PATHOGEN
|
RESULT
|
QC.STATUS
|
|
S-122-2
|
BVDv-Type-1
|
Negative
|
OK
|
|
S-122-2
|
BVDv-Type-2
|
Negative
|
OK
|
|
S-122-2
|
Bacillus licheniformis
|
Negative
|
OK
|
|
S-122-2
|
Bovine herpesvirus type-1
|
Positive
|
OK
|
|
S-122-2
|
BVDv
|
Negative
|
OK
|
|
S-122-2
|
Campylobacter fetus
|
Negative
|
OK
|
|
S-122-2
|
Campylobacter fetus subsp. venerealis
|
Negative
|
OK
|
|
S-122-2
|
Campylobacter jejuni subsp. jejuni
|
Negative
|
OK
|
|
S-122-2
|
Chlamydia abortus
|
Negative
|
OK
|
|
S-122-2
|
Coxiella burnetii
|
Positive
|
OK
|
|
S-122-2
|
Internal amplification control
|
Positive
|
OK
|
|
S-122-2
|
Leptospira borgpetersenii serovar. Hardjo
|
Negative
|
OK
|
|
S-122-2
|
Leptospira interrogans serovar. Copenhageni
|
Negative
|
OK
|
|
S-122-2
|
Leptospira kirschneri
|
Negative
|
OK
|
|
S-122-2
|
Listeria monocytogenes
|
Negative
|
OK
|
|
S-122-2
|
Mycoplasma bovis
|
Positive
|
OK
|
|
S-122-2
|
Neospora caninum
|
Negative
|
OK
|
|
S-122-2
|
Sarcocystis bovini
|
Negative
|
OK
|
|
S-122-2
|
Sarcocystis cruzi
|
Negative
|
OK
|
|
S-122-2
|
Sarcocystis hirsuta
|
Negative
|
OK
|
|
S-122-2
|
Toxoplasma gondii
|
Negative
|
OK
|
|
S-122-2
|
Tritrichomonas foetus
|
Negative
|
OK
|
|
S-122-2
|
Trueperella pyogenes
|
Positive
|
OK
|
|
S-122-2
|
Ureaplasma diversum
|
Negative
|
OK
|
NO. OF MAPPED READS. Generated using minimap2 and samtools
|
AMPLICON
|
MAPPED_READS
|
|
Coxiella_burnetti_Trans-1
|
20
|
|
IBR-gBN
|
18
|
|
IBR-gE
|
621
|
|
IC-EGFP
|
572
|
|
Trueperella_pyogenes_plo
|
400
|
|
Trueperella_pyogenes_sodA
|
109
|
|
Mbovis_PpSM5
|
139345
|
|
Mbovis_uvrC
|
13821
|
Consensus compared to reference database. Generated using abricate and custom database
|
SEQUENCE
|
GENE
|
%COVERAGE
|
%IDENTITY
|
DATABASE
|
REFERENCE
|
|
S-122-2_Coxiella_burnetti_Trans-1
|
Transposon-like_element
|
100.00
|
98.91
|
Bovreproseq
|
Coxiella_burnetii
|
|
S-122-2_IBR-gBN
|
gB-glycoprotein_B
|
100.00
|
100.00
|
Bovreproseq
|
Bovine_herpesvirus_type-1
|
|
S-122-2_IBR-gE
|
gE-glycoprotein_E
|
100.00
|
100.00
|
Bovreproseq
|
Bovine_herpesvirus_type-1
|
|
S-122-2_IC-EGFP
|
IC-EGFP
|
100.00
|
100.00
|
Bovreproseq
|
Internal_amplification_control
|
|
S-122-2_Mbovis_PpSM5
|
PPSM5
|
100.00
|
100.00
|
Bovreproseq
|
Mycoplasma_bovis
|
|
S-122-2_Mbovis_uvrC
|
uvrC-UV_excision_repair_gene
|
99.69
|
100.00
|
Bovreproseq
|
Mycoplasma_bovis
|
|
S-122-2_Trueperella_pyogenes_plo
|
PLO-Pyolysin
|
100.00
|
99.78
|
Bovreproseq
|
Trueperella_pyogenes
|
|
S-122-2_Trueperella_pyogenes_sodA
|
sodA-Superoxide_dismutase
|
100.00
|
100.00
|
Bovreproseq
|
Trueperella_pyogenes
|
>S-122-2_IC-EGFP_consensus
CAGCGTGTCCGGCGAGGGCGAGGGCGATGCCACCTACGGCAAGCTGACCCTGAAGTTCATCTGCACCACCGGCAAGCTGCCCGTGCCCTGGCCCACCCTCGTGACCACCCTGACCTACGGCGTGCAGTGCTTCAGCCGCTACCCCGACCACATGAAGCAGCACGACTTCTTCAAGTCCGCCATGCCCGAAGGCTACGTCCAGGAGCGCACCATCTTCTTCAAGGACGACGGCAACTACAAGACCCGCGCCGAGGTGAAGTTCGAGGGCGACACCCTGGTGAACCGCATCGAGCTGAAGGGCATCGACTTCAAGGAGGACGGCAACATCCTGGGGCACAAGCTGGAGTACAACTACAACAGCCACAACGTCTATATCATGGCCGACAAGCAGAAGAACGGCATCAAGGTGAACTTCAAGATCCGCCACAACATCGAGGACGGCAGCGTGCAGCTCGCCGACCACTACCAGCAGAACACCCCCATCGGCGACGGCCCCGTGCTGCTGCCCGA
>S-122-2_Mbovis_PpSM5_consensus
TTATCTCGGCTATACCTGAAAATGATGATGAGAGATTATTCTCAATTCAAGGAACCCCACCAGATATGGCAAACTTACCTATCGGTGACCCTTTTGCACCTAGAAATGACTTTGCCTTAGAAATTGACTATGAAAAAGAACCACCATTAATTGAAATTAATAGTCATCATAAAGCAGCAACGTGACTACTTCACCCTGATGCACCAAAAATACAAAGACCAAAAGAATTAGAACATAGACTAAAAAGTTTTAGAAAGGTATTTAAAGACGATGAAGAATAACGACAATAAAAAAGTCATTTTAGAAATTCAAGATCTTAAAAAGTACTTTTTAAATAACGGTAAGGTCAACAAAGCTGTTGATGGTGTGTCATTTAAATTACATGAAGG
>S-122-2_Trueperella_pyogenes_plo_consensus
TAGCTCGGGTCTTGTTCAGGATATCGGCATACTTAGCCTTGAACTCTGTGGAAAGATTGCCGAACTTAGCTTTGAACAGGCCGCTAAAAGCCGCTTGTACATCATTGGAAGTCGAGGTCGTTTCCAGCTTGACAAAAATCTGGCGTCCATAGCTGACCGACGAAATGTATCCTAGAGGATTCTTGTTATTGACTcCCCGATCTTTCAAATCCTGTGCGGTGACATTCGGGCCGAAAACGCTATGTGGAGATGTCGGTGTATCTACGCTAGCCGTGTAGTAAATCTGTTTGAAGGAAGCGATAGCCACCTGCCGTTCACGCTTATGAATTGCATCGAAGTCCACGTTGAGCTTGGCTGAGACCTTTTCAAATCCGAGGCCAAGCTTTGCCTCCAGTTGACGCTTTGACGTCACCATAGTCTCATCGTAAGAAATCTTTGCAGCATGGTCAGGATACTTGCTGTTGCGCTGAATCCAACCGTCGAGAAGGCCGTT
>S-122-2_IBR-gBN_consensus
TACATGTCGCCCTTTTACGGGCTGCGCGAGGGCGCGCACCGCGAGCACACCAGCTACTCGCCGGAGCGCTTCCAGCAGATCGAGGGCTACTACAAGCGCGACATGGCCACGGGCCGGCGCCTCAAGGAGCCGGTCTCGCGGAACTTTTTGCGTACACAGCACGTGACGGTAGCCTGGGACTGGGTGCCCAAGCGCAAAAACGTGTGCTCGCTGGCCAAGTGGCGCGAGGCGGACGAAATGCTGCGAGACGAGAGCCGCGGGAACTTCCGCTTCACGGCCCGCTCGCTCTCGGCGACCTTTGTGAGCGACAGCCACACCTTCGCGTTGCAGAATGTGCCGCTGAGC
>S-122-2_IBR-gE_consensus
CACGGCGCGCGCTGGCGCGCCCGTCtTTCTCCCAGGGCCCGCGGCGCGCCCGGACGTGCGCGCCGTTCGCGGCTGGAGCGTCCTCGCGGGCGCCTGCTCGCCGCCCGTGCCGGAGCCCGTCTGCCTCGACGACCGCGAGTGCTTCACCGACGTGGCCCTGGACGCGGCCTGCCTGCGAACCGCCCGCGTGGCCCCGCTGGCCATCGCGGAGCTCGCCGAGCGGCC
>S-122-2_Trueperella_pyogenes_sodA_consensus
CAACTGGCACGTTGGCCTGCTGGTCGAAAAGCTGGAACGTGATCAAGCCGCCCGAAATCGTGTCGTAGGCGAGCACGGCCCAGCCTGAGCCCTGGATGCCGGTAGCCACCGCGGTGAACTGCTTCTTGAAATCTTCGAATGATCCGAAAGC
>S-122-2_Coxiella_burnetti_Trans-1_consensus
TTAAGGTGGGCTGCGTGGTGATGGAAGCGTGTGGAGGAGCGAACCATTGGTATCGGACGTTTATGGGGATGGGTATCYCAACGCAGTTGATCAGTCCGCAGCACGTCAAACCGTATGTCAAAAGTAACAAGAATGATCGTAACGATGCGCAGGCGATAGCTGAAGCGGCTTCCCGCGCCTCGATGCGGTTTGTGCGGGGTAAAACGGTGGAACAACAAGACGTTCAAGCGCTGTTAAAGATACGCGATCGTTTAGTCAAAAGCCGCACGGCGCTGATCAATGAGATTCGGGGGTTGTTGCAAGAATACGGACTCACGATGGCgGCGTGGTGCCAAGCGATTTTATGAAGAGCTCCCGTTGATTTTAGCGAGCGAAGCGGTGGGATTAACACCGCGGATGAAACGGGTGTTGAATTGTTTGTATACCGAATTGTTGAACCGGGACGAAGCNATTGGTGATTACGAGGAGGAATTAAAAGCGGTGGCAAAAGCCAATGAGGATTGTCAACGGGTACAGAGCATCCCGGGGGTGGGTTATTTAACGGCGCTGTCGGTTTATGCGAGCGTGGGTGACATTCATCAATTTCATCGTTCCCGGCAGTTGTCGGCGTTTATTGGGTTGGTCCMTCGACAACATTCGAGKG
>S-122-2_Mbovis_uvrC_consensus
TATACTAATGGAATTAAAAACAAAAGCTTATATAGAAAATTTAATTTAGAAGCTTTAAATGAGCGCAGTGCTGATGTTGAATATATTAAGCAATCAATTTCTAAATTTTTTAGTAGCAACAAAAACACTAAAGATTATGACTTAGTTATAGCTGATGGCGGTATACAACAAGTTAATGAAGCTAAAAAAACGCTTAAAACGCTTAATATAAACATCCCTGTTATTGGATTAGTAAAAAATGAGTTTCACAAAACCAAAGCCTTAATTGACCTAGATATGAATGAAATTCATATTAATGACTTAGAACTATACAACTACTTAGTTC
Download FASTA file
RESULTS SUMMARY - Based on abricate results
|
SAMPLEID
|
PATHOGEN
|
RESULT
|
QC.STATUS
|
|
S-123-2
|
BVDv-Type-1
|
Negative
|
OK
|
|
S-123-2
|
BVDv-Type-2
|
Positive
|
OK
|
|
S-123-2
|
Bacillus licheniformis
|
Negative
|
OK
|
|
S-123-2
|
Bovine herpesvirus type-1
|
Positive
|
OK
|
|
S-123-2
|
BVDv
|
Positive
|
OK
|
|
S-123-2
|
Campylobacter fetus
|
Negative
|
OK
|
|
S-123-2
|
Campylobacter fetus subsp. venerealis
|
Negative
|
OK
|
|
S-123-2
|
Campylobacter jejuni subsp. jejuni
|
Negative
|
OK
|
|
S-123-2
|
Chlamydia abortus
|
Negative
|
OK
|
|
S-123-2
|
Coxiella burnetii
|
Negative
|
OK
|
|
S-123-2
|
Internal amplification control
|
Positive
|
OK
|
|
S-123-2
|
Leptospira borgpetersenii serovar. Hardjo
|
Negative
|
OK
|
|
S-123-2
|
Leptospira interrogans serovar. Copenhageni
|
Negative
|
OK
|
|
S-123-2
|
Leptospira kirschneri
|
Negative
|
OK
|
|
S-123-2
|
Listeria monocytogenes
|
Negative
|
OK
|
|
S-123-2
|
Mycoplasma bovis
|
Positive
|
OK
|
|
S-123-2
|
Neospora caninum
|
Negative
|
OK
|
|
S-123-2
|
Sarcocystis bovini
|
Negative
|
OK
|
|
S-123-2
|
Sarcocystis cruzi
|
Negative
|
OK
|
|
S-123-2
|
Sarcocystis hirsuta
|
Negative
|
OK
|
|
S-123-2
|
Toxoplasma gondii
|
Negative
|
OK
|
|
S-123-2
|
Tritrichomonas foetus
|
Negative
|
OK
|
|
S-123-2
|
Trueperella pyogenes
|
Positive
|
OK
|
|
S-123-2
|
Ureaplasma diversum
|
Positive
|
OK
|
NO. OF MAPPED READS. Generated using minimap2 and samtools
|
AMPLICON
|
MAPPED_READS
|
|
BVDv-2_5’UTR
|
509
|
|
IBR-gBN
|
241
|
|
IBR-gE
|
4119
|
|
IC-EGFP
|
391
|
|
Ureaplasmadiversum-16SrRNA
|
23182
|
|
Ureaplasmaspp_UGP
|
13098
|
|
Trueperella_pyogenes_plo
|
10
|
|
Trueperella_pyogenes_sodA
|
22
|
|
Mbovis_PpSM5
|
88388
|
|
Mbovis_uvrC
|
6905
|
Consensus compared to reference database. Generated using abricate and custom database
|
SEQUENCE
|
GENE
|
%COVERAGE
|
%IDENTITY
|
DATABASE
|
REFERENCE
|
|
S-123-2_BVDv-2_5’UTR
|
5’UTR
|
100.00
|
99.18
|
Bovreproseq
|
BVDv-Type-2
|
|
S-123-2_IBR-gBN
|
gB-glycoprotein_B
|
100.00
|
100.00
|
Bovreproseq
|
Bovine_herpesvirus_type-1
|
|
S-123-2_IBR-gE
|
gE-glycoprotein_E
|
100.00
|
100.00
|
Bovreproseq
|
Bovine_herpesvirus_type-1
|
|
S-123-2_IC-EGFP
|
IC-EGFP
|
100.00
|
100.00
|
Bovreproseq
|
Internal_amplification_control
|
|
S-123-2_Mbovis_PpSM5
|
PPSM5
|
100.00
|
100.00
|
Bovreproseq
|
Mycoplasma_bovis
|
|
S-123-2_Mbovis_uvrC
|
uvrC-UV_excision_repair_gene
|
99.69
|
100.00
|
Bovreproseq
|
Mycoplasma_bovis
|
|
S-123-2_Trueperella_pyogenes_plo
|
PLO-Pyolysin
|
100.00
|
99.78
|
Bovreproseq
|
Trueperella_pyogenes
|
|
S-123-2_Trueperella_pyogenes_sodA
|
sodA-Superoxide_dismutase
|
100.00
|
100.00
|
Bovreproseq
|
Trueperella_pyogenes
|
|
S-123-2_Ureaplasmadiversum-16SrRNA
|
UD-16SrRNA
|
100.00
|
100.00
|
Bovreproseq
|
Ureaplasma_diversum
|
|
S-123-2_Ureaplasmaspp_UGP
|
UGP-16SrRNA
|
100.00
|
99.83
|
Bovreproseq
|
Ureaplasma_diversum
|
>S-123-2_IC-EGFP_consensus
CAGCGTGTCCGGCGAGGGCGAGGGCGATGCCACCTACGGCAAGCTGACCCTGAAGTTCATCTGCACCACCGGCAAGCTGCCCGTGCCCTGGCCCACCCTCGTGACCACCCTGACCTACGGCGTGCAGTGCTTCAGCCGCTACCCCGACCACATGAAGCAGCACGACTTCTTCAAGTCCGCCATGCCCGAAGGCTACGTCCAGGAGCGCACCATCTTCTTCAAGGACGACGGCAACTACAAGACCCGCGCCGAGGTGAAGTTCGAGGGCGACACCCTGGTGAACCGCATCGAGCTGAAGGGCATCGACTTCAAGGAGGACGGCAACATCCTGGGGCACAAGCTGGAGTACAACTACAACAGCCACAACGTCTATATCATGGCCGACAAGCAGAAGAACGGCATCAAGGTGAACTTCAAGATCCGCCACAACATCGAGGACGGCAGCGTGCAGCTCGCCGACCACTACCAGCAGAACACCCCCATCGGCGACGGCCCCGTGCTGCTGCCCGA
>S-123-2_Ureaplasmadiversum-16SrRNA_consensus
TCGGTGTTGTAGCTAACGCATTAAATGATGTGCCTGGGTAGTACATTCGCAAGAATGAAACTCAAACGGAATTGACGGGGACCCGCACAAGTGGTGGAGCATGTTGCTTAATTTGACAATACACGTAGAACCTTACCTAGGTTTGACATCTATTGCAATGCTATAGAAATATAGCGGAGGTTAACAATATGACAGGTGGTGCATGGTTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCCTTTCGC
>S-123-2_Mbovis_PpSM5_consensus
TTATCTCGGCTATACCTGAAAATGATGATGAGAGATTATTCTCAATTCAAGGAACCCCACCAGATATGGCAAACTTACCTATCGGTGACCCTTTTGCACCTAGAAATGACTTTGCCTTAGAAATTGACTATGAAAAAGAACCACCATTAATTGAAATTAATAGTCATCATAAAGCAGCAACGTGACTACTTCACCCTGATGCACCAAAAATACAAAGACCAAAAGAATTAGAACATAGACTAAAAAGTTTTAGAAAGGTATTTAAAGACGATGAAGAATAACGACAATAAAAAAGTCATTTTAGAAATTCAAGATCTTAAAAAGTACTTTTTAAATAACGGTAAGGTCAACAAAGCTGTTGATGGTGTGTCATTTAAATTACATGAAGG
>S-123-2_Trueperella_pyogenes_plo_consensus
TAGCTCGGGTCTTGTTCAGGATATCGGCATACTTAGCCTTGAACTCTGTGGAAAGATTGCCGAACTTAGCTTTGAACAGGCCGCTAAAAGCCGCTTGTACATCATTGGAAGTCGAGGTCGTTTCCAGCTTGACAAAAATCTGGCGTCCATAGCTGACCGACGAAATGTATCCTAGAGGATTCTTGTTATTGACTCCCCGATCTTTCAAATCCTGTGCGGTGACATTCGGGCCGAAAACGCTATGTGGAGATGTCGGTGTATCTACGCTAGCCGTGTAGTAAATCTGTTTGAAGGAAGCGATAGCCACCTGCCGTTCACGCTTATGAATTGCATCGAAGTCCACGTTGAGCTTGGCTGAGACCTTTTCAAATCCGAGGCCAAGCTTTGCCTCCAGTTGACGCTTTGACGTCACCATAGTCTCATCGTAAGAAATCTTTGCAGCATGGTCAGGATACTTGCTGTTGCGCTGAATCCAACCGTCGAGAAGGCCGTT
>S-123-2_Trueperella_pyogenes_sodA_consensus
CAACTGGCACGTTGGCCTGCTGGTCGAAAAGCTGGAACGTGATCAAGCCGCCCGAAATCGTGTCGTAGGCGAGCACGGCCCAGCCTGAGCCCTGGATGCCGGTAGCCACCGCGGTGAACTGCTTCTTGAAATCTTCGAATGATCCGAAAGC
>S-123-2_IBR-gE_consensus
CACGGCGCGCGCTGGCGCGCCCGTCTTTCTCCCAGGGCCCGCGGCGCGCCCGGACGTGCGCGCCGTTCGCGGCTGGAGCGTCCTCGCGGGCGCCTGCTCGCCGCCCGTGCCGGAGCCCGTCTGCCTCGACGACCGCGAGTGCTTCACCGACGTGGCCCTGGACGCGGCCTGCCTGCGAACCGCCCGCGTGGCCCCGCTGGCCATCGCGGAGCTCGCCGAGCGGCC
>S-123-2_Mbovis_uvrC_consensus
TATACTAATGGAATTAAAAACAAAAGCTTATATAGAAAATTTAATTTAGAAGCTTTAAATGAGCGCAGTGCTGATGTTGAATATATTAAGCAATCAATTTCTAAATTTTTTAGTAGCAACAAAAACACTAAAGATTATGACTTAGTTATAGCTGATGGCGGTATACAACAAGTTAATGAAGCTAAAAAAACGCTTAAAACGCTTAATATAAACATCCCTGTTATTGGATTAGTAAAAAATGAGTTTCACAAAACCAAAGCCTTAATTGACCTAGATATGAATGAAATTCATATTAATGACTTAGAACTATACAACTACTTAGTTC
>S-123-2_BVDv-2_5'UTR_consensus
AAAAGGAGGGGACTAGCGGTAGCAGTGAGTTCATTGGATGGCCGAATCCCTGAGTACAGGGAAGTCGTCAGTGGTTCGACACTCCATCAACCGAGGAGTCTCGAGATGCCATGTGGACGAGGGCATGCCCACGGCACATCTTAACCTATGCGGGGGTTGCATGGGTGAAAGCACCATTCGTGGTGTTATGGACACAGCCTGATAGGGTGTAGCAGAGACCTGCTATTCCGCTAGTAAAAACTCTG
>S-123-2_IBR-gBN_consensus
TACATGTCGCCCTTTTACGGGCTGCGCGAGGGCGCGCACCGCGAGCACACCAGCTACTCGCCGGAGCGCTTCCAGCAGATCGAGGGCTACTACAAGCGCGACATGGCCACGGGCCGGCGCCTCAAGGAGCCGGTCTCGCGGAACTTTTTGCGTACACAGCACGTGACGGTAGCCTGGGACTGGGTGCCCAAGCGCAAAAACGTGTGCTCGCTGGCCAAGTGGCGCGAGGCGGACGAAATGCTGCGAGACGAGAGCCGCGGGAACTTCCGCTTCACGGCCCGCTCGCTCTCGGCGACCTTTGTGAGCGACAGCCACACCTTCGCGTTGCAGAATGTGCCGCTGAGC
>S-123-2_Ureaplasmaspp_UGP_consensus
AGATAGTTGGTGAGGTAACGGCTCACCAAGTCATTGACGCGTAGCTGTACTGAGAGGTAGAACAGCCACAATGGGACTGAGACACGGCCCATACTCCTACGGGAGGCAGCAGTAGGGAATTTTTCACAATGGGCGAAAGCCTTATGAAGCAATGCCGCGTGAACGATGAAGGTCTATAAGATTGTAAAGTTCTTTTATTTGGGAAGAACCACTAAAATAGGAAATGATTTTAGTTTGACTGTACCATTTGAATAAGTATCGGCTAACTATGTGCCAGCAGCCGCGGTAATACATAGGATGCAAGCGTTATCCGGATTTACTGGGCGTAAAACGAGCGCAGGCGGATTTGTAAGTTTGGTATGAAATCTAGATGCTTAACGTCTAGCTGTATCAAAAACTACGAATCTAGAGTGTAGCAGAGAGTTGGGGAACTCCATGTGGAGCGGTAAAATGCGTAGATATATGGAAGAACACCGGTGGCGAAGGCGCCAACTTGGACTATTACTGACGCTTAGGCTCGAAAGTGTGGGGAGCAAATAGGATTAGATACCCTAGTAGTCCACACCGTAAACGATCATCATTAAATGTCGGCTCGCTTATGA
Download FASTA file
RESULTS SUMMARY - Based on abricate results
|
SAMPLEID
|
PATHOGEN
|
RESULT
|
QC.STATUS
|
|
S-175-4
|
BVDv-Type-1
|
Negative
|
Check for PCR inhibition
|
|
S-175-4
|
BVDv-Type-2
|
Negative
|
Check for PCR inhibition
|
|
S-175-4
|
Bacillus licheniformis
|
Negative
|
Check for PCR inhibition
|
|
S-175-4
|
Bovine herpesvirus type-1
|
Negative
|
Check for PCR inhibition
|
|
S-175-4
|
BVDv
|
Negative
|
Check for PCR inhibition
|
|
S-175-4
|
Campylobacter fetus
|
Negative
|
Check for PCR inhibition
|
|
S-175-4
|
Campylobacter fetus subsp. venerealis
|
Negative
|
Check for PCR inhibition
|
|
S-175-4
|
Campylobacter jejuni subsp. jejuni
|
Negative
|
Check for PCR inhibition
|
|
S-175-4
|
Chlamydia abortus
|
Negative
|
Check for PCR inhibition
|
|
S-175-4
|
Coxiella burnetii
|
Negative
|
Check for PCR inhibition
|
|
S-175-4
|
Internal amplification control
|
Negative
|
Check for PCR inhibition
|
|
S-175-4
|
Leptospira borgpetersenii serovar. Hardjo
|
Negative
|
Check for PCR inhibition
|
|
S-175-4
|
Leptospira interrogans serovar. Copenhageni
|
Negative
|
Check for PCR inhibition
|
|
S-175-4
|
Leptospira kirschneri
|
Negative
|
Check for PCR inhibition
|
|
S-175-4
|
Listeria monocytogenes
|
Negative
|
Check for PCR inhibition
|
|
S-175-4
|
Mycoplasma bovis
|
Negative
|
Check for PCR inhibition
|
|
S-175-4
|
Neospora caninum
|
Negative
|
Check for PCR inhibition
|
|
S-175-4
|
Sarcocystis bovini
|
Negative
|
Check for PCR inhibition
|
|
S-175-4
|
Sarcocystis cruzi
|
Negative
|
Check for PCR inhibition
|
|
S-175-4
|
Sarcocystis hirsuta
|
Negative
|
Check for PCR inhibition
|
|
S-175-4
|
Toxoplasma gondii
|
Negative
|
Check for PCR inhibition
|
|
S-175-4
|
Tritrichomonas foetus
|
Negative
|
Check for PCR inhibition
|
|
S-175-4
|
Trueperella pyogenes
|
Positive
|
Check for PCR inhibition
|
|
S-175-4
|
Ureaplasma diversum
|
Negative
|
Check for PCR inhibition
|
NO. OF MAPPED READS. Generated using minimap2 and samtools
|
AMPLICON
|
MAPPED_READS
|
|
Trueperella_pyogenes_sodA
|
689
|
Consensus compared to reference database. Generated using abricate and custom database
|
SEQUENCE
|
GENE
|
%COVERAGE
|
%IDENTITY
|
DATABASE
|
REFERENCE
|
|
S-175-4_Trueperella_pyogenes_sodA
|
sodA-Superoxide_dismutase
|
100
|
99.34
|
Bovreproseq
|
Trueperella_pyogenes
|
>S-175-4_Trueperella_pyogenes_sodA_consensus
CAACTGGCACGTTGGCCTGCTGGTCGAAAAGCTGGAACGTGATCAAGCCGCCCGAAATCGTGTCGTAGGCGAGCACGGCCCAGCCTGAGCCCTGGATGCCGGTAGCCACCGCGGTGAACTGCCTCTTGAAATCTTCGAATGATCCGAAAGC
Download FASTA file
RESULTS SUMMARY - Based on abricate results
|
SAMPLEID
|
PATHOGEN
|
RESULT
|
QC.STATUS
|
|
S-266-3
|
BVDv-Type-1
|
Negative
|
OK
|
|
S-266-3
|
BVDv-Type-2
|
Positive
|
OK
|
|
S-266-3
|
Bacillus licheniformis
|
Negative
|
OK
|
|
S-266-3
|
Bovine herpesvirus type-1
|
Negative
|
OK
|
|
S-266-3
|
BVDv
|
Positive
|
OK
|
|
S-266-3
|
Campylobacter fetus
|
Negative
|
OK
|
|
S-266-3
|
Campylobacter fetus subsp. venerealis
|
Negative
|
OK
|
|
S-266-3
|
Campylobacter jejuni subsp. jejuni
|
Negative
|
OK
|
|
S-266-3
|
Chlamydia abortus
|
Negative
|
OK
|
|
S-266-3
|
Coxiella burnetii
|
Negative
|
OK
|
|
S-266-3
|
Internal amplification control
|
Positive
|
OK
|
|
S-266-3
|
Leptospira borgpetersenii serovar. Hardjo
|
Negative
|
OK
|
|
S-266-3
|
Leptospira interrogans serovar. Copenhageni
|
Negative
|
OK
|
|
S-266-3
|
Leptospira kirschneri
|
Negative
|
OK
|
|
S-266-3
|
Listeria monocytogenes
|
Negative
|
OK
|
|
S-266-3
|
Mycoplasma bovis
|
Positive
|
OK
|
|
S-266-3
|
Neospora caninum
|
Negative
|
OK
|
|
S-266-3
|
Sarcocystis bovini
|
Negative
|
OK
|
|
S-266-3
|
Sarcocystis cruzi
|
Negative
|
OK
|
|
S-266-3
|
Sarcocystis hirsuta
|
Negative
|
OK
|
|
S-266-3
|
Toxoplasma gondii
|
Negative
|
OK
|
|
S-266-3
|
Tritrichomonas foetus
|
Negative
|
OK
|
|
S-266-3
|
Trueperella pyogenes
|
Negative
|
OK
|
|
S-266-3
|
Ureaplasma diversum
|
Positive
|
OK
|
NO. OF MAPPED READS. Generated using minimap2 and samtools
|
AMPLICON
|
MAPPED_READS
|
|
BVDv-2_5’UTR
|
99
|
|
IC-EGFP
|
815
|
|
Ureaplasmadiversum-16SrRNA
|
29912
|
|
Ureaplasmaspp_UGP
|
26984
|
|
Mbovis_PpSM5
|
13602
|
|
Mbovis_uvrC
|
229
|
Consensus compared to reference database. Generated using abricate and custom database
|
SEQUENCE
|
GENE
|
%COVERAGE
|
%IDENTITY
|
DATABASE
|
REFERENCE
|
|
S-266-3_BVDv-2_5’UTR
|
5’UTR
|
100.00
|
94.69
|
Bovreproseq
|
BVDv-Type-2
|
|
S-266-3_IC-EGFP
|
IC-EGFP
|
100.00
|
100.00
|
Bovreproseq
|
Internal_amplification_control
|
|
S-266-3_Mbovis_PpSM5
|
PPSM5
|
100.00
|
99.23
|
Bovreproseq
|
Mycoplasma_bovis
|
|
S-266-3_Mbovis_uvrC
|
uvrC-UV_excision_repair_gene
|
99.69
|
97.84
|
Bovreproseq
|
Mycoplasma_bovis
|
|
S-266-3_Ureaplasmadiversum-16SrRNA
|
UD-16SrRNA
|
100.00
|
100.00
|
Bovreproseq
|
Ureaplasma_diversum
|
|
S-266-3_Ureaplasmaspp_UGP
|
UGP-16SrRNA
|
100.00
|
99.83
|
Bovreproseq
|
Ureaplasma_diversum
|
>S-266-3_IC-EGFP_consensus
CAGCGTGTCCGGCGAGGGCGAGGGCGATGCCACCTACGGCAAGCTGACCCTGAAGTTCATCTGCACCACCGGCAAGCTGCCCGTGCCCTGGCCCACCCTCGTGACCACCCTGACCTACGGCGTGCAGTGCTTCAGCCGCTACCCCGACCACATGAAGCAGCACGACTTCTTCAAGTCCGCCATGCCCGAAGGCTACGTCCAGGAGCGCACCATCTTCTTCAAGGACGACGGCAACTACAAGACCCGCGCCGAGGTGAAGTTCGAGGGCGACACCCTGGTGAACCGCATCGAGCTGAAGGGCATCGACTTCAAGGAGGACGGCAACATCCTGGGGCACAAGCTGGAGTACAACTACAACAGCCACAACGTCTATATCATGGCCGACAAGCAGAAGAACGGCATCAAGGTGAACTTCAAGATCCGCCACAACATCGAGGACGGCAGCGTGCAGCTCGCCGACCACTACCAGCAGAACACCCCCATCGGCGACGGCCCCGTGCTGCTGCCCGA
>S-266-3_Mbovis_PpSM5_consensus
TTATCTCGGCTATACCTGAAAATGATGATGAGAGATTATTCTCAATTCAAGGAACCCCACCAGATATGGCAAACTTACCTATCGGTGACCCTTTTGCGCCTAGAAATGACTTTGCTTTAGAAATTGACTATGAAAAAGAACCACCATTAATTGAAATTAATAGTCATCATAAAGCAGCAACGTGACTACTTCACCCTGATGCACCAAAAATACAAAGACCAAAAGAATTAGAACATAGACTAAAAAGTTTTAGAAAGGTATTTAAAGACGATGAAGAATAACGACAATAAAAAAGTCATTTTAGAAATTCAAGATCTTAAAAAGTACTTTTTAAACAACGGTAAGGTCAACAAAGCTGTTGATGGTGTGTCATTTAAATTACATGAAGG
>S-266-3_Ureaplasmadiversum-16SrRNA_consensus
TCGGTGTTGTAGCTAACGCATTAAATGATGTGCCTGGGTAGTACATTCGCAAGAATGAAACTCAAACGGAATTGACGGGGACCCGCACAAGTGGTGGAGCATGTTGCTTAATTTGACAATACACGTAGAACCTTACCTAGGTTTGACATCTATTGCAATGCTATAGAAATATAGCGGAGGTTAACAATATGACAGGTGGTGCATGGTTGTCGTCAGCTCGTGTCGTGAGATGTTGGGTTAAGTCCCGCAACGAGCGCAACCCCTTTCGC
>S-266-3_Mbovis_uvrC_consensus
TATACTAATGGAATTAAAAACAAAAGCTTATATAGAAAATTTAATTTAGAAGCTTTAAATGAGCGCAGTGCTGATGTTGAATATATTAAGCAATCAATTTCTAAATTTTTTAGTAGCAACAAAAACACTAAAGATTATGACTTAGTTATAGCTGATGGTGGTGTACAACAAGTTAATGAAGCTAAAAAAACGCTTAAAACACTTAATATAAACATCCCTGTTATTGGATTAGTAAAAAATGAGTTTCACAAAACTAAAGCCTTAATTGACCTAGATATGAATGAAATTCACATTTCTGACTTAGAACTATACAACTACTTAGTTC
>S-266-3_BVDv-2_5'UTR_consensus
AAAAATAGGGGACTAGCGGTAGCAGTGAGTTCATTGGATGGCCGAACCCCTGAGTACAGGGGAGTCGTCAATGGTTCGACACTCCATTGGTTGAGGAGTCTCGAGATGCCATGTGGACGAGGGCATGCCCACGGCACATCTTAACCCATGCGGGGGTTGCATGGGTGAAAGCGCTATTCATGGCGTTATGGACACAGCCTGATAGGGTGTAGCAGAGACCTGCTATTCCGCTAGTAAAAACTCTG
>S-266-3_Ureaplasmaspp_UGP_consensus
AGATAGTTGGTGAGGTAACGGCTCACCAAGTCATTGACGCGTAGCTGTACTGAGAGGTAGAACAGCCACAATGGGACTGAGACACGGCCCATACTCCTACGGGAGGCAGCAGTAGGGAATTTTTCACAATGGGCGAAAGCCTTATGAAGCAATGCCGCGTGAACGATGAAGGTCTATAAGATTGTAAAGTTCTTTTATTTGGGAAGAACCACTAAAATAGGAAATGATTTTAGTTTGACTGTACCATTTGAATAAGTATCGGCTAACTATGTGCCAGCAGCCGCGGTAATACATAGGATGCAAGCGTTATCCGGATTTACTGGGCGTAAAACGAGCGCAGGCGGATTTGTAAGTTTGGTATGAAATCTAGATGCTTAACGTCTAGCTGTATCAAAAACTACGAATCTAGAGTGTAGCAGAGAGTTGGGGAACTCCATGTGGAGCGGTAAAATGCGTAGATATATGGAAGAACACCGGTGGCGAAGGCGCCAACTTGGACTATTACTGACGCTTAGGCTCGAAAGTGTGGGGAGCAAATAGGATTAGATACCCTAGTAGTCCACACCGTAAACGATCATCATTAAATGTCGGCTCGCTTATGA
Download FASTA file
RESULTS SUMMARY - Based on abricate results
|
SAMPLEID
|
PATHOGEN
|
RESULT
|
QC.STATUS
|
|
S-363
|
BVDv-Type-1
|
Negative
|
OK
|
|
S-363
|
BVDv-Type-2
|
Negative
|
OK
|
|
S-363
|
Bacillus licheniformis
|
Negative
|
OK
|
|
S-363
|
Bovine herpesvirus type-1
|
Negative
|
OK
|
|
S-363
|
BVDv
|
Negative
|
OK
|
|
S-363
|
Campylobacter fetus
|
Negative
|
OK
|
|
S-363
|
Campylobacter fetus subsp. venerealis
|
Negative
|
OK
|
|
S-363
|
Campylobacter jejuni subsp. jejuni
|
Negative
|
OK
|
|
S-363
|
Chlamydia abortus
|
Negative
|
OK
|
|
S-363
|
Coxiella burnetii
|
Negative
|
OK
|
|
S-363
|
Internal amplification control
|
Positive
|
OK
|
|
S-363
|
Leptospira borgpetersenii serovar. Hardjo
|
Negative
|
OK
|
|
S-363
|
Leptospira interrogans serovar. Copenhageni
|
Negative
|
OK
|
|
S-363
|
Leptospira kirschneri
|
Negative
|
OK
|
|
S-363
|
Listeria monocytogenes
|
Negative
|
OK
|
|
S-363
|
Mycoplasma bovis
|
Negative
|
OK
|
|
S-363
|
Neospora caninum
|
Negative
|
OK
|
|
S-363
|
Sarcocystis bovini
|
Negative
|
OK
|
|
S-363
|
Sarcocystis cruzi
|
Positive
|
OK
|
|
S-363
|
Sarcocystis hirsuta
|
Negative
|
OK
|
|
S-363
|
Toxoplasma gondii
|
Negative
|
OK
|
|
S-363
|
Tritrichomonas foetus
|
Negative
|
OK
|
|
S-363
|
Trueperella pyogenes
|
Negative
|
OK
|
|
S-363
|
Ureaplasma diversum
|
Negative
|
OK
|
NO. OF MAPPED READS. Generated using minimap2 and samtools
|
AMPLICON
|
MAPPED_READS
|
|
IC-EGFP
|
210690
|
|
Coccidia_Sarcocystiscruzi
|
661
|
Consensus compared to reference database. Generated using abricate and custom database
|
SEQUENCE
|
GENE
|
%COVERAGE
|
%IDENTITY
|
DATABASE
|
REFERENCE
|
|
S-363_Coccidia_Sarcocystiscruzi
|
Coccidia-18SrRNA
|
83.27
|
92.37
|
Bovreproseq
|
Sarcocystis_cruzi
|
|
S-363_IC-EGFP
|
IC-EGFP
|
100.00
|
100.00
|
Bovreproseq
|
Internal_amplification_control
|
>S-363_IC-EGFP_consensus
CAGCGTGTCCGGCGAGGGCGAGGGCGATGCCACCTACGGCAAGCTGACCCTGAAGTTCATCTGCACCACCGGCAAGCTGCCCGTGCCCTGGCCCACCCTCGTGACCACCCTGACCTACGGCGTGCAGTGCTTCAGCCGCTACCCCGACCACATGAAGCAGCACGACTTCTTCAAGTCCGCCATGCCCGAAGGCTACGTCCAGGAGCGCACCATCTTCTTCAAGGACGACGGCAACTACAAGACCCGCGCCGAGGTGAAGTTCGAGGGCGACACCCTGGTGAACCGCATCGAGCTGAAGGGCATCGACTTCAAGGAGGACGGCAACATCCTGGGGCACAAGCTGGAGTACAACTACAACAGCCACAACGTCTATATCATGGCCGACAAGCAGAAGAACGGCATCAAGGTGAACTTCAAGATCCGCCACAACATCGAGGACGGCAGCGTGCAGCTCGCCGACCACTACCAGCAGAACACCCCCATCGGCGACGGCCCCGTGCTGCTGCCCGA
>S-363_Coccidia_Sarcocystiscruzi_consensus
TGCACTTGATGAATTCTGGCATCTATGTCCCAATAgtATGTGATGGTGTAtaTATACCCTGTGtataTAYtAttatMCCATCTATATTGGGATAATACCGTTACTTTGAGAAAATTAGAGTGTTTGAAGCAGGCTAATTGCCTTGAATACTGCAGCATGGAATAACAATATAGGATTTCGGTTCTATTTTGTTGGTTTCTAGGACTGAAATAATGATTAATAGGGACAGTTGGGGGCATTCGTATTTAA
Download FASTA file
RESULTS SUMMARY - Based on abricate results
|
SAMPLEID
|
PATHOGEN
|
RESULT
|
QC.STATUS
|
|
S-443
|
BVDv-Type-1
|
Negative
|
OK
|
|
S-443
|
BVDv-Type-2
|
Negative
|
OK
|
|
S-443
|
Bacillus licheniformis
|
Negative
|
OK
|
|
S-443
|
Bovine herpesvirus type-1
|
Negative
|
OK
|
|
S-443
|
BVDv
|
Negative
|
OK
|
|
S-443
|
Campylobacter fetus
|
Negative
|
OK
|
|
S-443
|
Campylobacter fetus subsp. venerealis
|
Negative
|
OK
|
|
S-443
|
Campylobacter jejuni subsp. jejuni
|
Negative
|
OK
|
|
S-443
|
Chlamydia abortus
|
Negative
|
OK
|
|
S-443
|
Coxiella burnetii
|
Negative
|
OK
|
|
S-443
|
Internal amplification control
|
Positive
|
OK
|
|
S-443
|
Leptospira borgpetersenii serovar. Hardjo
|
Negative
|
OK
|
|
S-443
|
Leptospira interrogans serovar. Copenhageni
|
Negative
|
OK
|
|
S-443
|
Leptospira kirschneri
|
Negative
|
OK
|
|
S-443
|
Listeria monocytogenes
|
Negative
|
OK
|
|
S-443
|
Mycoplasma bovis
|
Negative
|
OK
|
|
S-443
|
Neospora caninum
|
Negative
|
OK
|
|
S-443
|
Sarcocystis bovini
|
Negative
|
OK
|
|
S-443
|
Sarcocystis cruzi
|
Positive
|
OK
|
|
S-443
|
Sarcocystis hirsuta
|
Negative
|
OK
|
|
S-443
|
Toxoplasma gondii
|
Negative
|
OK
|
|
S-443
|
Tritrichomonas foetus
|
Negative
|
OK
|
|
S-443
|
Trueperella pyogenes
|
Negative
|
OK
|
|
S-443
|
Ureaplasma diversum
|
Negative
|
OK
|
NO. OF MAPPED READS. Generated using minimap2 and samtools
|
AMPLICON
|
MAPPED_READS
|
|
IC-EGFP
|
125536
|
|
Coccidia_Sarcocystiscruzi
|
2013
|
Consensus compared to reference database. Generated using abricate and custom database
|
SEQUENCE
|
GENE
|
%COVERAGE
|
%IDENTITY
|
DATABASE
|
REFERENCE
|
|
S-443_Coccidia_Sarcocystiscruzi
|
Coccidia-18SrRNA
|
100
|
85.06
|
Bovreproseq
|
Sarcocystis_cruzi
|
|
S-443_IC-EGFP
|
IC-EGFP
|
100
|
100.00
|
Bovreproseq
|
Internal_amplification_control
|
>S-443_IC-EGFP_consensus
CAGCGTGTCCGGCGAGGGCGAGGGCGATGCCACCTACGGCAAGCTGACCCTGAAGTTCATCTGCACCACCGGCAAGCTGCCCGTGCCCTGGCCCACCCTCGTGACCACCCTGACCTACGGCGTGCAGTGCTTCAGCCGCTACCCCGACCACATGAAGCAGCACGACTTCTTCAAGTCCGCCATGCCCGAAGGCTACGTCCAGGAGCGCACCATCTTCTTCAAGGACGACGGCAACTACAAGACCCGCGCCGAGGTGAAGTTCGAGGGCGACACCCTGGTGAACCGCATCGAGCTGAAGGGCATCGACTTCAAGGAGGACGGCAACATCCTGGGGCACAAGCTGGAGTACAACTACAACAGCCACAACGTCTATATCATGGCCGACAAGCAGAAGAACGGCATCAAGGTGAACTTCAAGATCCGCCACAACATCGAGGACGGCAGCGTGCAGCTCGCCGACCACTACCAGCAGAACACCCCCATCGGCGACGGCCCCGTGCTGCTGCCCGA
>S-443_Coccidia_Sarcocystiscruzi_consensus
AGTTGGATGTCTGCTGAAAGCAGTNGGNCCCCNNCCCNATTTGTAGGGTGTGCACTTGATGAATTCTGGCATCTATGTCCCAATRgtATRTGAYGGTGtataTAgTAtYcYTGgcgaaWGtataTWYtAttatMCCWTccgTWTATTGGGATAATACYGTTACTTTGAGAAAATTAGAGTGTTTGAAGCAGGCTAATTGCCTTGAATACTGCAGCATGGAATAACAATATAGGATTTCGGTTCTATTTTGTTGGTTTCTAGGACTGAAATAATGATTAATAGGGACAGTTGGGGGCATTCGTATTTAA
Download FASTA file
RESULTS SUMMARY - Based on abricate results
|
SAMPLEID
|
PATHOGEN
|
RESULT
|
QC.STATUS
|
|
S-615
|
BVDv-Type-1
|
Negative
|
OK
|
|
S-615
|
BVDv-Type-2
|
Negative
|
OK
|
|
S-615
|
Bacillus licheniformis
|
Negative
|
OK
|
|
S-615
|
Bovine herpesvirus type-1
|
Negative
|
OK
|
|
S-615
|
BVDv
|
Negative
|
OK
|
|
S-615
|
Campylobacter fetus
|
Positive
|
OK
|
|
S-615
|
Campylobacter fetus subsp. venerealis
|
Positive
|
OK
|
|
S-615
|
Campylobacter jejuni subsp. jejuni
|
Negative
|
OK
|
|
S-615
|
Chlamydia abortus
|
Negative
|
OK
|
|
S-615
|
Coxiella burnetii
|
Negative
|
OK
|
|
S-615
|
Internal amplification control
|
Positive
|
OK
|
|
S-615
|
Leptospira borgpetersenii serovar. Hardjo
|
Negative
|
OK
|
|
S-615
|
Leptospira interrogans serovar. Copenhageni
|
Negative
|
OK
|
|
S-615
|
Leptospira kirschneri
|
Negative
|
OK
|
|
S-615
|
Listeria monocytogenes
|
Negative
|
OK
|
|
S-615
|
Mycoplasma bovis
|
Negative
|
OK
|
|
S-615
|
Neospora caninum
|
Negative
|
OK
|
|
S-615
|
Sarcocystis bovini
|
Negative
|
OK
|
|
S-615
|
Sarcocystis cruzi
|
Negative
|
OK
|
|
S-615
|
Sarcocystis hirsuta
|
Negative
|
OK
|
|
S-615
|
Toxoplasma gondii
|
Negative
|
OK
|
|
S-615
|
Tritrichomonas foetus
|
Negative
|
OK
|
|
S-615
|
Trueperella pyogenes
|
Negative
|
OK
|
|
S-615
|
Ureaplasma diversum
|
Negative
|
OK
|
NO. OF MAPPED READS. Generated using minimap2 and samtools
|
AMPLICON
|
MAPPED_READS
|
|
CampylobacterfetusMLST-aspA
|
5172
|
|
CampylobacterfetusMLST-glnA
|
5993
|
|
CampylobacterfetusMLST-gltA
|
8172
|
|
CampylobacterfetusMLST-glyA
|
909
|
|
CampylobacterfetusMLST-pgm
|
3586
|
|
CampylobacterfetusMLST-tkt
|
8253
|
|
CampylobacterfetusMLST-uncA
|
29151
|
|
CFF_nahE
|
1987
|
|
CFV_parA
|
16118
|
|
IC-EGFP
|
11506
|
Consensus compared to reference database. Generated using abricate and custom database
|
SEQUENCE
|
GENE
|
%COVERAGE
|
%IDENTITY
|
DATABASE
|
REFERENCE
|
|
S-615_CFF_nahE
|
hydratase-aldolase_nahE
|
100
|
100
|
Bovreproseq
|
Campylobacter_fetus
|
|
S-615_CFV_parA
|
parA-partitioning_protein_A
|
100
|
100
|
Bovreproseq
|
Campylobacter_fetus_subsp._venerealis
|
|
S-615_CampylobacterfetusMLST-aspA
|
aspA-aspartase_A
|
100
|
100
|
Bovreproseq
|
Campylobacter_fetus
|
|
S-615_CampylobacterfetusMLST-glnA
|
glnA-glutamine_synthetase
|
100
|
100
|
Bovreproseq
|
Campylobacter_fetus
|
|
S-615_CampylobacterfetusMLST-gltA
|
gltA-citrate_synthase
|
100
|
100
|
Bovreproseq
|
Campylobacter_fetus
|
|
S-615_CampylobacterfetusMLST-glyA
|
glyA-serine_hydroxymethyltransferase
|
100
|
100
|
Bovreproseq
|
Campylobacter_fetus
|
|
S-615_CampylobacterfetusMLST-pgm
|
pgm-phosphoglucomutase
|
100
|
100
|
Bovreproseq
|
Campylobacter_fetus
|
|
S-615_CampylobacterfetusMLST-tkt
|
tkt-transketolase
|
100
|
100
|
Bovreproseq
|
Campylobacter_fetus
|
|
S-615_CampylobacterfetusMLST-uncA
|
uncA-ATP_synthase_alpha_subunit
|
100
|
100
|
Bovreproseq
|
Campylobacter_fetus
|
|
S-615_IC-EGFP
|
IC-EGFP
|
100
|
100
|
Bovreproseq
|
Internal_amplification_control
|
MLST tool from github (https://github.com/tseemann/mlst). Scans contig files against traditional PubMLST typing schemes
|
FILE
|
ST
|
ORGANISM
|
|
S-615_medaka_consensus.fasta
|
4
|
Campylobacter fetus. venerealis
|
>S-615_IC-EGFP_consensus
CAGCGTGTCCGGCGAGGGCGAGGGCGATGCCACCTACGGCAAGCTGACCCTGAAGTTCATCTGCACCACCGGCAAGCTGCCCGTGCCCTGGCCCACCCTCGTGACCACCCTGACCTACGGCGTGCAGTGCTTCAGCCGCTACCCCGACCACATGAAGCAGCACGACTTCTTCAAGTCCGCCATGCCCGAAGGCTACGTCCAGGAGCGCACCATCTTCTTCAAGGACGACGGCAACTACAAGACCCGCGCCGAGGTGAAGTTCGAGGGCGACACCCTGGTGAACCGCATCGAGCTGAAGGGCATCGACTTCAAGGAGGACGGCAACATCCTGGGGCACAAGCTGGAGTACAACTACAACAGCCACAACGTCTATATCATGGCCGACAAGCAGAAGAACGGCATCAAGGTGAACTTCAAGATCCGCCACAACATCGAGGACGGCAGCGTGCAGCTCGCCGACCACTACCAGCAGAACACCCCCATCGGCGACGGCCCCGTGCTGCTGCCCGA
>S-615_CFV_parA_consensus
TTGCGGTTGGATTATAAATTTTAGCTTGGTTGAAAACTAAAATCATCTTATTTAATACCGCAATATCAAGATCGCTTGGGATAACTGGGAT
>S-615_CampylobacterfetusMLST-glnA_consensus
TTGGCAGCCGATTCATAAATCAGATATGATGCTAAAACCAGATGTAGAAACTGCGTTTTTAGATCCTTTTACTGCAGATACGACTATTATAGTAATATGTGATGTTTATGACATATACAAAGGTGAATTATATGAAAAATGTCCTAGAAGTATAGCAAAAAAGGCATCGCAATATCTAAGAGATAGCGGTGTAGGAGACGTAGCTTACTTTGGACCTGAAAATGAGTTTTTTGTATTTGACAATGTTCGCATTATAGATAAACCAAATTGCGCTATGTATGAAGTAGATACGGAAGAAGGCGAGTGGAATGATGGTAAAGAGTATACAGATGGATACAATACGGGTCACAGACCACGCACCAAAGGTGGATATTTTCCAGTTCAACCAGTCGATAGCATGGTGGATCTAAGAGCTGAAATGGTAAATGTACTTGAACAAGTAGGACTTGAAACTTTTGTGGTTCATCATGAAGTTGCTCAAGGACAAGGCGAAATAGGCGTCAAATTCGGCACACTTGTAGAGGCTGCGGATAATGTTCAAATTTATAAATATGTAGTAAAAATGGTAGCTCATCTAAACGGTAAAACAGCTACATTTATGCCAAAACCG
>S-615_CampylobacterfetusMLST-uncA_consensus
GAACTGAGCAAAAGCTTGAAGTTCGCGATACTGAGCAAGATCAAGCCTTAGTGTTCCAGAAACTTTTTTAATAGCTTTTATCTGGGCTGATCCGCCGACACGACTAACAGACAAACCAACGTTAATAGCAGGACGAATACCTGAGTTAAACAAGTCGCTTTCCAAGAAAATTTGACCATCAGTTATAGAAATAACATTTGTAGGAATATACGCTGAAACGTCACCTGCTTGAGTCTCGATAATAGGTAGAGCCGTAAGACTTCCCGCTCCTAGTTTATCACTTAGCTTACTAGCTCTCTCAAGCAGTCTTGAGTGCAGATAGAAAACATCTCCTGGATATGCTTCACGACCCGGCGGTCTTCTTAAAATCAATGACATTTCACGGTAAGCTACAGCGTGCTTGCTTAGATCATCATAAATAATAAGAGCATGGCGTGAGTTATCACGGAAATATTCACCCATTGTTACACCTGCATATGGAGCAAGATATTGTAACGCCGGAGCATCGCTTGCACTTGCATTAACTACTATAGTATA
>S-615_CampylobacterfetusMLST-gltA_consensus
AAAATAAACTTTATCTTGATGTAGTATATTTACTATTTAACAAACACCTGCCAAGCCAAGAGGAGCTGGAGCTATTTAGACGCGAGTTAAAAGAGAGAAGCTTTTTAAATGAAAAAATGATTAGATTATTTGACTGTTTTCCCGATAAAGCTCATCCTATGGCCGTTTTACAAGCAAGCGTAGCTACCATGAGTGCATACTATAAAAGAGATATGAATTTTGATGATATGAATGATTATATGGAGCTTGCAAAACGTTTAGTGGCAAAAATTCCTACATTTATAGCGTTTTATTATCGTCATGTTAGAGGATTTCCTGTAATATATCCGAATTTAGATCGCGGATTTACAGAAAATTTCTTATATATGCTAAGAGCTTTTCCTCACGATAAGGTAGATTTAAAACCTATAGAAGTCAAGGCTTTTGATACTGTTTTGATGCTTCACGCTGATCATGAACAAAATGCTTCAACTACTACAGTTAGAA
>S-615_CampylobacterfetusMLST-aspA_consensus
TTTAAAACTTTTGCTATCATGCTTGGCGAAGATATCGACCGTGTAAGAGAAGCTAGAAACTTAGTACGCGAGATAAACCTAGGCGGAACAGCTATCGGTACAGGTATCAACTCTCACCCAGACTATCCAAAAGTAGTCGAGACAAAACTTCAAGAAGTAACAAAACGTCCATTCATCACTGCTGGTAACCTTATAGAAGCTACTCAAGACACAGGCGCTTATGTTCAAATTTCAGGCGTTTTAAAAAGAGTTAGTACAAAACTAAGCAAAATTTGTAATGACTTAAGACTTTTAAGCAGCGGCCCAAGATGCGGACTAAACGAGATAAACTTACCAAAAATGCAACCGGGCTCAAGCATTATGCCAGGCAAAGTAAATCCTGTTATCCCTGAAGTAGTAAATCAAGTTTGTTTCGCAGTTATCGGTAATGACGTAACTGTAACTCTAGCTAGCGAAGGCGGACAACTTCAACTAAACGTATTTGAACCAGTTATCGCTTATAGTCTGTTTAACTCTATCGCAATGCTTAAAAAA
>S-615_CampylobacterfetusMLST-tkt_consensus
TGGTCATGCAAGTAGCTTGGTTTATAGTTATTTATATCTTTGTGGTTATGACGTTAGTTTGGATGATTTGAAAAAATTTAGACAACTTCACTCTAAAACTCCCGGACATCCCGAGATAGAAACCCCGGGAGTAGAGATAGCAACTGGACCATTAGGACAAGGAGTGGCAAATGCTGTAGGTTTTGCCATGGCGGCAAAAAGCGCTTCAAATTTACTTGGAAATGAGATTATAAATCATAAAGTATATTGTCTGTGCGGCGATGGAGATCTAGAAGAAGGTATCAGTTATGAAGCTTGTGCTTTGGCTGGAAAACACTCTTTAGATAATTTAGTGATTATATATGATAGCAATAATATCACGATAGAGGGCGATACTAGTATAGCGTGGTGTGAAGATGTAAAAGTACGTTTTGAAGCGGCTGGATTTGAAGTTGCGCGGATAGATGGACATAATTATGATGAGATTGAATTTGCACTTTGCGAAGCAGATACGAAAGAAAAACCTTATCTTATTATCGCAAGTACAAAGATTGCTAAAGGCGC
>S-615_CFF_nahE_consensus
AACTTTGAGATAATATTTGAAAATTTATTAATGATAATAGTGATTTTGGTCGATGTTATGGTGATCAAAATAGCTGTTGTATATGCACTTTTAGCAACTTATCTTaAAAAAAGAGTAGCCATAAAAACAGCTCTTAGTATATGTCAGATTGGCGAGTTCGCTTTAGCTATTTTTGCTCTTTTAAACGTAAATAATATGTTAAATTCAGAAACTTCTCAAATTTTAACCGCGGTTGTAATTATATCTATGGTAGCTACTCCGTTGATCTTaAAAAACATCGGACATTTAGCCGACAGACTAGAAGAAGAGAGCGAAATACCTGAGTT
>S-615_CampylobacterfetusMLST-pgm_consensus
TTTTCTATAATTTTCAAATTTGAAAGTTTTTGTGGATATGCTTTAATACTCCCGAATATCTCGCTGGCTTTTTTATTTTTAGCTAAGAGACAAGCGCTTACTTGCAAAGCTGAAACAAGTCCGTCGCCGGTCTTTGAAAAATCGCTAAATATGATGTGTCCGCTCTGCTCACCGCCGAAATTTATGCCGTTTTCTTTCATCATTTCAAGAACGAATTTATCTCCGACGTTTGAACGAAGAAGCTTAATTTTGTGTTTTGCAAGATAGTCGTCAAGTGCGGCATTACTCATCACGGTGGCTACTATCTCCTTTTTATCAAGCATCTTATTTTCATCAAGATAAGTAGCCAAAACGCCGAGCAAAGCGTCTCCATCGACAACTTTTGCATTTTCATCGACAACCACAAGTCTATCGGCATCACCGTCAAAAGCAAATCCTATATCGGCTCTTAATCTTTTAACTTCTTTTGCCAAATTTTCAGGATGCAAAGCACCGCAGCCATCATTTATATTTCCGCCGTTTGGTTCATCGTTTAAAACTATTGTCTCTGCTCCAAGCTCGCTAAATACGGTCGGAGCGACTTTATAAACTGCGCCGTTT
>S-615_CampylobacterfetusMLST-glyA_consensus
CCGAGTTTTTTAGCGTTTGTCTTTACTTGCTTAGCATAAACTTTCCACTCGTCACTAAGATTATGCTTAAATCCAACTGCTTTTCCAGCAATCACGTGCATAAGCGGCCCGCCTTGAATTCCCGGAAATATAGAACTATTTATTTTTTTAGCAAATTCCTCATCATTTGTCATGATGATACCGCCTCTTGGACCTCTTAATGTTTTATGAGTAGTTGAACTTACAACGTGACAGTGAGGAAATGGATTGTTATGTTCTCCTGCTACTACAAGACCTGCTATATGAGCAACATCGGCAAATAAATATGCTCCAACGCTATCGGCTATCTCTCTAAATTTCTTAAAATCAATCTCTCTAGCATAAGCACTAGCACCGCAAACTATCATTTTAGGTTTAGTTATATTTGCTATCTCTTCTACTTTATTATAATTTATACGTCCATCAAGCTCAACACCGTAGAAAAAGCTCTCATAGTTTTTTCCAGAGCTTGAAACTTTAGAACCGTGAGTAAGGTGTCCACCATGGCTTA
Download FASTA file
RESULTS SUMMARY - Based on abricate results
|
SAMPLEID
|
PATHOGEN
|
RESULT
|
QC.STATUS
|
|
S-805-2
|
BVDv-Type-1
|
Positive
|
OK
|
|
S-805-2
|
BVDv-Type-2
|
Negative
|
OK
|
|
S-805-2
|
Bacillus licheniformis
|
Negative
|
OK
|
|
S-805-2
|
Bovine herpesvirus type-1
|
Negative
|
OK
|
|
S-805-2
|
BVDv
|
Positive
|
OK
|
|
S-805-2
|
Campylobacter fetus
|
Negative
|
OK
|
|
S-805-2
|
Campylobacter fetus subsp. venerealis
|
Negative
|
OK
|
|
S-805-2
|
Campylobacter jejuni subsp. jejuni
|
Negative
|
OK
|
|
S-805-2
|
Chlamydia abortus
|
Negative
|
OK
|
|
S-805-2
|
Coxiella burnetii
|
Negative
|
OK
|
|
S-805-2
|
Internal amplification control
|
Positive
|
OK
|
|
S-805-2
|
Leptospira borgpetersenii serovar. Hardjo
|
Negative
|
OK
|
|
S-805-2
|
Leptospira interrogans serovar. Copenhageni
|
Negative
|
OK
|
|
S-805-2
|
Leptospira kirschneri
|
Negative
|
OK
|
|
S-805-2
|
Listeria monocytogenes
|
Negative
|
OK
|
|
S-805-2
|
Mycoplasma bovis
|
Negative
|
OK
|
|
S-805-2
|
Neospora caninum
|
Negative
|
OK
|
|
S-805-2
|
Sarcocystis bovini
|
Positive
|
OK
|
|
S-805-2
|
Sarcocystis cruzi
|
Negative
|
OK
|
|
S-805-2
|
Sarcocystis hirsuta
|
Negative
|
OK
|
|
S-805-2
|
Toxoplasma gondii
|
Negative
|
OK
|
|
S-805-2
|
Tritrichomonas foetus
|
Negative
|
OK
|
|
S-805-2
|
Trueperella pyogenes
|
Negative
|
OK
|
|
S-805-2
|
Ureaplasma diversum
|
Negative
|
OK
|
NO. OF MAPPED READS. Generated using minimap2 and samtools
|
AMPLICON
|
MAPPED_READS
|
|
BVDv_Npro
|
126
|
|
BVDv-1_5’UTR
|
21442
|
|
IC-EGFP
|
34208
|
|
Sarcocystis_spp
|
389
|
|
Coccidia_Spp.
|
11
|
Consensus compared to reference database. Generated using abricate and custom database
|
SEQUENCE
|
GENE
|
%COVERAGE
|
%IDENTITY
|
DATABASE
|
REFERENCE
|
|
S-805-2_BVDv-1_5’UTR
|
5’UTR
|
98.78
|
90.12
|
Bovreproseq
|
BVDv-Type-1
|
|
S-805-2_BVDv_Npro
|
Npro-N-terminal_autoprotease
|
97.69
|
81.84
|
Bovreproseq
|
BVDv
|
|
S-805-2_Coccidia_Spp.
|
Coccidia-18SrRNA
|
99.68
|
88.58
|
Bovreproseq
|
Aspergillus_fumigatus_isolate
|
|
S-805-2_IC-EGFP
|
IC-EGFP
|
100.00
|
100.00
|
Bovreproseq
|
Internal_amplification_control
|
|
S-805-2_Sarcocystis_spp
|
Sarcocystis-18SrRNA
|
86.72
|
93.32
|
Bovreproseq
|
Sarcocystis_bovini
|
>S-805-2_IC-EGFP_consensus
CAGCGTGTCCGGCGAGGGCGAGGGCGATGCCACCTACGGCAAGCTGACCCTGAAGTTCATCTGCACCACCGGCAAGCTGCCCGTGCCCTGGCCCACCCTCGTGACCACCCTGACCTACGGCGTGCAGTGCTTCAGCCGCTACCCCGACCACATGAAGCAGCACGACTTCTTCAAGTCCGCCATGCCCGAAGGCTACGTCCAGGAGCGCACCATCTTCTTCAAGGACGACGGCAACTACAAGACCCGCGCCGAGGTGAAGTTCGAGGGCGACACCCTGGTGAACCGCATCGAGCTGAAGGGCATCGACTTCAAGGAGGACGGCAACATCCTGGGGCACAAGCTGGAGTACAACTACAACAGCCACAACGTCTATATCATGGCCGACAAGCAGAAGAACGGCATCAAGGTGAACTTCAAGATCCGCCACAACATCGAGGACGGCAGCGTGCAGCTCGCCGACCACTACCAGCAGAACACCCCCATCGGCGACGGCCCCGTGCTGCTGCCCGA
>S-805-2_Sarcocystis_spp_consensus
TTACTTTGAGAAAATTAGAGTGTTTGAAGCAGGCAATTGCCTTGAATACTGCAGCATGGAATAACAACATAGGATTTCGGTTCTATTTTGTTGGTTTCAGGACTGAAATAATGATTAATAGGGACAGTCGGGGGCATTCGTATTTAACTGTCAGAGGTGAAATTCTTAGATTTGTAAAGACGAACAACTGCGAAAGCATTTGCCAAGGATGTTTTCATTAATCAAGAACGAAAGTTAGGGGCTCGAAGACGATCAGATACCGTCCTAGTCTCAACCATAAACGATGCCGACCAGGGATCGGCGGATGTTGCTTATAGGACTCCGCCGGCACCTTATGAGAAATCAAAGTTTTTGGGTTCCGGGGGGAGTATGGTCGCAAGGCTGAAACTTAAAGGAATTGACGGAAGGGCACCACCAGGAGTGGAGCCTGCGGCTTAATTTGACTCAACACGGGGAAACTTACCAGGTCCAGACATAGTAAGGATTGACAGACTGAGAGCTCTT
>S-805-2_BVDv_Npro_consensus
GGCACATGGAGTTGATCACAAATGAACTTTTATACAAAACATACAAACAAAAACCCACTGGAGTGGAGGAACCAGTATACGACCAAGCTGGTAACCCTTTGTTTGGAGAAAGAGGAGAGATTCATCCGCAGTCAACGCTAAAACTGCCACATAAAAGAGGGGCACGCGAAGTACCCACCAATTTGGCTTCTTTACCAAAAAGAGGTGACTGCAGGTCGGGTAACAGCAAGGGGCCTGTGAGTGGAATCTACTTAAAACCAGGGCCGTTATTCTACCAGGATTATAAAGGACCTGTCTATCATAGAGCCCCATTGGAGTTTTTTGAAGAAGCGTCTATGTGTGAGATAACCAAAAGAATCGGGAGAGTAACTGGTAGTGACAGCAAATTA
>S-805-2_Coccidia_Spp._consensus
GTTGTTGCAGTTAAAAAGCTSGTAGTTGAAACTTGGGcYCNGGCTGGCAGGTCCGCCTCACCGCGTGTACTTgccggccGNNCGGNCKGGCctTTCCTTCTGGAGAACCTCATGCCCTTCACTGGGtgGTGTKggKKgggAACCAGGACTTTTACTTTGAAAAAATTAGAGTGTTCAAAGCAGGCCTTTGCTCGAATACGTTAGCATGGAATAATAGAATAGGACGTGCGGTCCTATTTTGTTGGTTTCTAGGACCGCCGTAATGATTAATAGGGACAGTNGGGGGCATCAGTATTCAANTGTCAGAGGTGAAATTCTTAGAT
>S-805-2_BVDv-1_5'UTR_consensus
AAAATAAGGGGGGTAGCAACAGTGGTGAGTTTGTTGGATGGCTGAAGCCCTGAGTACAGGGTAGTCGTCAGTGGTTCGACGCTTTGGAGAATGAGCCTCGAGATGCCACGTGGACGAGGGCATGCCCACAGCACATCTTAGCCTGGACGGGGGTCGTTCAGGTGAAAACGGTTTAATCAACCGCTACGAATACAGCCTGATAGGGTGCTGCAGAGGCCCACTGTATTGCTACTAAAAATCTCTG
Download FASTA file
RESULTS SUMMARY - Based on abricate results
|
SAMPLEID
|
PATHOGEN
|
RESULT
|
QC.STATUS
|
|
S-807-4
|
BVDv-Type-1
|
Negative
|
OK
|
|
S-807-4
|
BVDv-Type-2
|
Negative
|
OK
|
|
S-807-4
|
Bacillus licheniformis
|
Negative
|
OK
|
|
S-807-4
|
Bovine herpesvirus type-1
|
Negative
|
OK
|
|
S-807-4
|
BVDv
|
Negative
|
OK
|
|
S-807-4
|
Campylobacter fetus
|
Negative
|
OK
|
|
S-807-4
|
Campylobacter fetus subsp. venerealis
|
Negative
|
OK
|
|
S-807-4
|
Campylobacter jejuni subsp. jejuni
|
Negative
|
OK
|
|
S-807-4
|
Chlamydia abortus
|
Negative
|
OK
|
|
S-807-4
|
Coxiella burnetii
|
Positive
|
OK
|
|
S-807-4
|
Internal amplification control
|
Positive
|
OK
|
|
S-807-4
|
Leptospira borgpetersenii serovar. Hardjo
|
Negative
|
OK
|
|
S-807-4
|
Leptospira interrogans serovar. Copenhageni
|
Negative
|
OK
|
|
S-807-4
|
Leptospira kirschneri
|
Negative
|
OK
|
|
S-807-4
|
Listeria monocytogenes
|
Negative
|
OK
|
|
S-807-4
|
Mycoplasma bovis
|
Negative
|
OK
|
|
S-807-4
|
Neospora caninum
|
Negative
|
OK
|
|
S-807-4
|
Sarcocystis bovini
|
Negative
|
OK
|
|
S-807-4
|
Sarcocystis cruzi
|
Negative
|
OK
|
|
S-807-4
|
Sarcocystis hirsuta
|
Negative
|
OK
|
|
S-807-4
|
Toxoplasma gondii
|
Negative
|
OK
|
|
S-807-4
|
Tritrichomonas foetus
|
Negative
|
OK
|
|
S-807-4
|
Trueperella pyogenes
|
Negative
|
OK
|
|
S-807-4
|
Ureaplasma diversum
|
Negative
|
OK
|
NO. OF MAPPED READS. Generated using minimap2 and samtools
|
AMPLICON
|
MAPPED_READS
|
|
Coxiella_burnetti_COM1
|
51
|
|
Coxiella_burnetti_Trans-1
|
7666
|
|
IC-EGFP
|
5190
|
|
Sarcocystis_spp
|
42
|
Consensus compared to reference database. Generated using abricate and custom database
|
SEQUENCE
|
GENE
|
%COVERAGE
|
%IDENTITY
|
DATABASE
|
REFERENCE
|
|
S-807-4_Coxiella_burnetti_COM1
|
com1-Outer_membrane_protein
|
100.00
|
99.85
|
Bovreproseq
|
Coxiella_burnetii
|
|
S-807-4_Coxiella_burnetti_Trans-1
|
Transposon-like_element
|
99.69
|
99.53
|
Bovreproseq
|
Coxiella_burnetii
|
|
S-807-4_IC-EGFP
|
IC-EGFP
|
100.00
|
100.00
|
Bovreproseq
|
Internal_amplification_control
|
|
S-807-4_Sarcocystis_spp
|
Sarcocystis-18SrRNA
|
100.00
|
100.00
|
Bovreproseq
|
Oryza_glumipatula
|
>S-807-4_IC-EGFP_consensus
CAGCGTGTCCGGCGAGGGCGAGGGCGATGCCACCTACGGCAAGCTGACCCTGAAGTTCATCTGCACCACCGGCAAGCTGCCCGTGCCCTGGCCCACCCTCGTGACCACCCTGACCTACGGCGTGCAGTGCTTCAGCCGCTACCCCGACCACATGAAGCAGCACGACTTCTTCAAGTCCGCCATGCCCGAAGGCTACGTCCAGGAGCGCACCATCTTCTTCAAGGACGACGGCAACTACAAGACCCGCGCCGAGGTGAAGTTCGAGGGCGACACCCTGGTGAACCGCATCGAGCTGAAGGGCATCGACTTCAAGGAGGACGGCAACATCCTGGGGCACAAGCTGGAGTACAACTACAACAGCCACAACGTCTATATCATGGCCGACAAGCAGAAGAACGGCATCAAGGTGAACTTCAAGATCCGCCACAACATCGAGGACGGCAGCGTGCAGCTCGCCGACCACTACCAGCAGAACACCCCCATCGGCGACGGCCCCGTGCTGCTGCCCGA
>S-807-4_Coxiella_burnetti_COM1_consensus
ACTGCAGGCGTGGCGATAGCCGCCCCCTCTCAATCCAGTTTTTCTCCTCAACAAGTCAAAGACATACAAAGCATCGTCCACCATTATTTAGTCAACCACCCAGAAGTTTTAGTAGAAGCATCCCAAGCATTGCAAAAAAAGACAGAAGCGCAACAAGAAGAACACGCTCAACAAGCAATTAAAGAAAATGCAAAGAAATTATTTAACGACCCTGCATCACCAGTGGCAGGCAATCCTCATGGCAATGTTACATTGGTTGAATTTTTCGATTATCAATGTGGCCATTGCAAAGCCATGAATTCTGTTATTCAAGCTATCGTGAAACAAAATAAAAACCTCCGCGTTGTCTTCAAAGAACTGCCCATTTTTGGCGGCCAATCGCAATACGCTGCCAAAGTATCATTAGCAGCCGCTAAACAAGGAAAATATTATGCTTTCCACGACGCGCTGCTCAGTGTCGACGGCCAATTATCAGAACAAATCACCCTTCAAACCGCAGAAAAAGTAGGATTAAATGTTGCTCAGCTCAAAAAAGACATGGATAATCCTGCTATCCAAAAACAACTGCGTGATAACTTCCAATTAGCTCAATCGTTACAGCTAGCAGGCACCCCGACGTTCGTCATTGGTAATAAAGCGTTAACCAAATTCGGTTTTATACCCGGCGCCACCTCACAACAAAACCTTCA
>S-807-4_Sarcocystis_spp_consensus
GTTACTTTGAAGAAATTAGAGTGCTCAAAGCAAGCCATCGCTCTGGATACATTAGCATGGGATAACATCATAGGATTCCGGTCCTATTGTGTTGGCCTTCGGGATCGGAGTAATGATTAATAGGGACAGTCGGGGGCATTCGTATTTCATAGTCAGAGGTGAAATTCTTGGATTTATGAAAGACGAACAACTGCGAAAGCATTTGCCAAGGATGTTTTCATTAATCAAGAACGAAAGTTGGGGGCTCGAAGACGATCAGATACCGTCCTAGTCTCAACCATAAACGATGCCGACCAGGGATCGGCGGATGTTGCTTATAGGACTCCGCCGGCACCTTATGAGAAATCAAAGTCTTTGGGTTCCGGGGGGAGTATGGTCGCAAGGCTGAAACTTAAAGGAATTGACGGAAGGGCACCACCAGGCGTGGAGCCTGCGGCTTAATTTGACTCAACACGGGGAAACTTACCAGGTCCAGACATAGCAAGGATTGACAGACTGAGAGCTCTT
>S-807-4_Coxiella_burnetti_Trans-1_consensus
TTAAGGTGGGCTGCGTGGTGATGGAAGCGTGTGGAGGAGCGAACCATTGGTATCGGACGTTTATGGGGATGGGTATCTCAACGCAGTTGATCAGTCCGCAGCACGTCAAACCGTATGTCAAAAGTAACAAGAATGATCGTAACGATGCGCAGGCGATAGCTGAAGCGGCTTCCCGCGCCTCGATGCGGTTTGTGCGGGGTAAAACGGTGGAACAACAAGACGTTCAAGCGCTGTTAAAGATACGCGATCGTTTAGTCAAAAGCCGCACGGCGCTGATCAATGAGATTCGGGGGTTGTTGCAAGAATACGGACTCACGATGGCGCGTGGTGCCAAGCGATTTTATGAAGAGCTCCCGTTGATTTTAGCGAGCGAAGCGGTGGGATTAACACCGCGGATGAAACGGGTGTTGAATTGTTTGTATACCGAATTGTTGAACCGGGACGAAGCGATTGGTGATTACGAGGAGGAATTAAAAGCGGTGGCAAAAGCCAATGAGGATTGTCAACGGGTACAGAGCATCCCGGGGGTGGGTTATTTAACGGCGCTGTCGGTTTATGCGAGCGTGGGTGACATTCATCAATTTCATCGTTCCCGGCAGTTGTCGGCGTTTATTGGGTTGGTCCCTCGACAACATTCGAGGG
Download FASTA file
RESULTS SUMMARY - Based on abricate results
|
SAMPLEID
|
PATHOGEN
|
RESULT
|
QC.STATUS
|
|
S-907-1
|
BVDv-Type-1
|
Negative
|
OK
|
|
S-907-1
|
BVDv-Type-2
|
Negative
|
OK
|
|
S-907-1
|
Bacillus licheniformis
|
Negative
|
OK
|
|
S-907-1
|
Bovine herpesvirus type-1
|
Negative
|
OK
|
|
S-907-1
|
BVDv
|
Negative
|
OK
|
|
S-907-1
|
Campylobacter fetus
|
Positive
|
OK
|
|
S-907-1
|
Campylobacter fetus subsp. venerealis
|
Negative
|
OK
|
|
S-907-1
|
Campylobacter jejuni subsp. jejuni
|
Negative
|
OK
|
|
S-907-1
|
Chlamydia abortus
|
Negative
|
OK
|
|
S-907-1
|
Coxiella burnetii
|
Negative
|
OK
|
|
S-907-1
|
Internal amplification control
|
Positive
|
OK
|
|
S-907-1
|
Leptospira borgpetersenii serovar. Hardjo
|
Negative
|
OK
|
|
S-907-1
|
Leptospira interrogans serovar. Copenhageni
|
Negative
|
OK
|
|
S-907-1
|
Leptospira kirschneri
|
Negative
|
OK
|
|
S-907-1
|
Listeria monocytogenes
|
Negative
|
OK
|
|
S-907-1
|
Mycoplasma bovis
|
Negative
|
OK
|
|
S-907-1
|
Neospora caninum
|
Negative
|
OK
|
|
S-907-1
|
Sarcocystis bovini
|
Negative
|
OK
|
|
S-907-1
|
Sarcocystis cruzi
|
Negative
|
OK
|
|
S-907-1
|
Sarcocystis hirsuta
|
Negative
|
OK
|
|
S-907-1
|
Toxoplasma gondii
|
Negative
|
OK
|
|
S-907-1
|
Tritrichomonas foetus
|
Negative
|
OK
|
|
S-907-1
|
Trueperella pyogenes
|
Negative
|
OK
|
|
S-907-1
|
Ureaplasma diversum
|
Negative
|
OK
|
NO. OF MAPPED READS. Generated using minimap2 and samtools
|
AMPLICON
|
MAPPED_READS
|
|
CampylobacterfetusMLST-aspA
|
10332
|
|
CampylobacterfetusMLST-glnA
|
13154
|
|
CampylobacterfetusMLST-gltA
|
15633
|
|
CampylobacterfetusMLST-glyA
|
3763
|
|
CampylobacterfetusMLST-pgm
|
8812
|
|
CampylobacterfetusMLST-tkt
|
7938
|
|
CampylobacterfetusMLST-uncA
|
87447
|
|
CFF_nahE
|
5915
|
|
IC-EGFP
|
96481
|
Consensus compared to reference database. Generated using abricate and custom database
|
SEQUENCE
|
GENE
|
%COVERAGE
|
%IDENTITY
|
DATABASE
|
REFERENCE
|
|
S-907-1_CFF_nahE
|
hydratase-aldolase_nahE
|
100
|
99.39
|
Bovreproseq
|
Campylobacter_fetus
|
|
S-907-1_CampylobacterfetusMLST-aspA
|
aspA-aspartase_A
|
100
|
100.00
|
Bovreproseq
|
Campylobacter_fetus
|
|
S-907-1_CampylobacterfetusMLST-glnA
|
glnA-glutamine_synthetase
|
100
|
100.00
|
Bovreproseq
|
Campylobacter_fetus
|
|
S-907-1_CampylobacterfetusMLST-gltA
|
gltA-citrate_synthase
|
100
|
100.00
|
Bovreproseq
|
Campylobacter_fetus
|
|
S-907-1_CampylobacterfetusMLST-glyA
|
glyA-serine_hydroxymethyltransferase
|
100
|
100.00
|
Bovreproseq
|
Campylobacter_fetus
|
|
S-907-1_CampylobacterfetusMLST-pgm
|
pgm-phosphoglucomutase
|
100
|
100.00
|
Bovreproseq
|
Campylobacter_fetus
|
|
S-907-1_CampylobacterfetusMLST-tkt
|
tkt-transketolase
|
100
|
99.82
|
Bovreproseq
|
Campylobacter_fetus
|
|
S-907-1_CampylobacterfetusMLST-uncA
|
uncA-ATP_synthase_alpha_subunit
|
100
|
99.63
|
Bovreproseq
|
Campylobacter_fetus
|
|
S-907-1_IC-EGFP
|
IC-EGFP
|
100
|
100.00
|
Bovreproseq
|
Internal_amplification_control
|
MLST tool from github (https://github.com/tseemann/mlst). Scans contig files against traditional PubMLST typing schemes
|
FILE
|
ST
|
ORGANISM
|
|
S-907-1_medaka_consensus.fasta
|
2
|
Campylobacter fetus. fetus
|
>S-907-1_IC-EGFP_consensus
CAGCGTGTCCGGCGAGGGCGAGGGCGATGCCACCTACGGCAAGCTGACCCTGAAGTTCATCTGCACCACCGGCAAGCTGCCCGTGCCCTGGCCCACCCTCGTGACCACCCTGACCTACGGCGTGCAGTGCTTCAGCCGCTACCCCGACCACATGAAGCAGCACGACTTCTTCAAGTCCGCCATGCCCGAAGGCTACGTCCAGGAGCGCACCATCTTCTTCAAGGACGACGGCAACTACAAGACCCGCGCCGAGGTGAAGTTCGAGGGCGACACCCTGGTGAACCGCATCGAGCTGAAGGGCATCGACTTCAAGGAGGACGGCAACATCCTGGGGCACAAGCTGGAGTACAACTACAACAGCCACAACGTCTATATCATGGCCGACAAGCAGAAGAACGGCATCAAGGTGAACTTCAAGATCCGCCACAACATCGAGGACGGCAGCGTGCAGCTCGCCGACCACTACCAGCAGAACACCCCCATCGGCGACGGCCCCGTGCTGCTGCCCGA
>S-907-1_CampylobacterfetusMLST-aspA_consensus
TTTAAAACTTTTGCTATCATGCTTGGCGAAGATATCGACCGTGTAAGAGAAGCTAGAAACTTAGTACGCGAGATAAACCTAGGCGGAACAGCTATCGGTACAGGTATCAACTCTCACCCAGACTATCCAAAAGTAGTCGAGACAAAACTTCAAGAAGTAACAAAACGTCCATTCATCACTGCTGGTAACCTTATAGAAGCTACTCAAGACACAGGCGCTTATGTTCAAATTTCAGGCGTTTTAAAAAGAGTTAGTACAAAACTAAGCAAAATTTGTAATGACTTAAGACTTTTAAGCAGCGGCCCAAGATGCGGACTAAACGAGATAAACTTACCAAAAATGCAACCGGGCTCAAGCATTATGCCAGGCAAAGTAAATCCTGTTATCCCTGAAGTAGTAAATCAAGTTTGTTTCGCAGTTATCGGTAATGACGTAACTGTAACTCTAGCTAGCGAAGGCGGACAACTTCAACTAAACGTATTTGAACCAGTTATCGCTTATAGTCTGTTTAACTCTATCGCAATGCTTaAAAAAA
>S-907-1_CampylobacterfetusMLST-glnA_consensus
TTGGCAGCCGATTCATAAATCAGATATGATGCTAAAACCAGATGTAGAAACTGCGTTTTTAGATCCTTTTACTGCAGATACGACTATTATAGTAATATGTGATGTTTATGACATATACAAAGGTGAATTATATGAAAAATGTCCTAGAAGTATAGCAAAAAAGGCATCGCAATATCTAAGAGATAGCGGTGTAGGAGACGTAGCTTACTTTGGACCTGAAAATGAGTTTTTTGTATTTGACAATGTTCGCATTATAGATAAACCAAATTGCGCTATGTATGAAGTAGATACGGAAGAAGGCGAGTGGAATGATGGTAAAGAGTATACAGATGGATACAATACGGGTCACAGACCACGCACCAAAGGTGGATATTTTCCAGTTCAACCAGTCGATAGCATGGTGGATCTAAGAGCTGAAATGGTAAATGTACTTGAACAAGTAGGACTTGAAACTTTTGTGGTTCATCATGAAGTTGCTCAAGGACAAGGCGAAATAGGCGTCAAATTCGGCACACTTGTAGAGGCTGCGGATAATGTTCAAATTTATAAATATGTAGTAAAAATGGTAGCTCATCTAAACGGTAAAACAGCTACATTTATGCCAAAACCG
>S-907-1_CampylobacterfetusMLST-gltA_consensus
AAAATAAACTTTATCTTGATGTAGTATATTTACTATTTAACAAACACCTGCCAAGCCAAGAGGAGCTGGAGCTATTTAGACGCGAGTTAAAAGAGAGAAGCTTTTTAAATGAAAAAATGATTAGATTATTTGACTGTTTTCCCGATAAAGCTCATCCTATGGCCGTTTTACAAGCAAGCGTAGCTACCATGAGTGCATACTATAAAAGAGATATGAATTTTGATGATATGAATGATTATATGGAGCTTGCAAAACGTTTAGTGGCAAAAATTCCTACATTTATAGCGTTTTATTATCGTCATGTTAGAGGATTTCCTGTAATATATCCGAATTTAGATCGCGGATTTACAGAAAATTTCTTATATATGCTAAGAGCTTTTCCTCACGATAAGGTAGATTTAAAACCTATAGAAGTCAAGGCTTTTGATACTGTTTTGATGCTTCACGCTGATCATGAACAAAATGCTTCAACTACTACAGTTAGAA
>S-907-1_CampylobacterfetusMLST-tkt_consensus
TGGTCATGCAAGTAGCTTGGTTTATAGTTATTTATATCTTTGTGGTTATGACGTTAGTTTGGATGATTTGAAAAAATTTAGACAACTTCACTCTAAAACTCCCGGACATCCCGAGATAGAAACCCCGGGAGTAGAGATAGCAACTGGACCATTAGGACAAGGAGTGGCAAATGCTGTAGGTTTTGCCATGGCGGCAAAAAGCGCTTCAAATTTACTTGGAAATGAGATTATAAATCATAAAGTATATTGTCTGTGCGGCGATGGAGATCTAGAAGAAGGTATCAGTTATGAAGCTTGTGCTTTGGCTGGAAAACACTCTTTAGATAATTTAGTGATTATATATGATAGCAATAATATCACGATAGAGGGCGATACTAGTATAGCGTGGTGTGAAGATGTAAAAGTACGTTTTGAAGCGGCTGGATTTGAGGTTGCGCGGATAGATGGACATAATTATGATGAGATTGAATTTGCACTTTGCGAAGCAGATACGAAAGAAAAACCTTATCTTATTATCGCAAGTACAAAGATTGCTAAAGGCGC
>S-907-1_CampylobacterfetusMLST-pgm_consensus
TTTTCTATAATTTTCAAATTTGAAAGTTTTTGTGGATATGCTTTAATACTCCCGAATATCTCGCTGGCTTTTTTATTTTTAGCTAAGAGACAAGCGCTTACTTGCAAAGCTGAAACAAGTCCGTCGCCGGTCTTTGAAAAATCGCTAAATATGATGTGTCCGCTCTGCTCACCGCCGAAATTTATGCCGTTTTCTTTCATCATTTCAAGAACGAATTTATCTCCGACGTTTGAACGAAGAAGCTTAATTTTGTGTTTTGCAAGATAGTCGTCAAGTGCGGCATTACTCATCACGGTGGCTACTATCTCCTTTTTATCAAGCATCTTATTTTCATCAAGATAAGTAGCCAAAACGCCGAGCAAAGCGTCTCCATCGACAACTTTTGCATTTTCATCGACAACCACAAGTCTATCGGCATCACCGTCAAAAGCAAATCCTATATCGGCTCTTAATCTTTTAACTTCTTTTGCCAAATTTTCAGGATGCAAAGCACCGCAGCCATCATTTATATTTCCGCCGTTTGGTTCATCGTTTAAAACTATTGTCTCTGCTCCAAGCTCGCTAAATACGGTCGGAGCGACTTTATAAACTGCGCCGTTT
>S-907-1_CFF_nahE_consensus
AACTTTGAGATAATATTTGAAAATTTATTAATGATAATAGTGATTTTGGTCGATGTTATGGTGATCAAAATAGCTGTTGTATATGCACTTTTAGCAACTTATCTTaAAAAAAGAGTAGCCATAAAAACAGCTCTTAGTATATGTCAGATTGGCGAGTTCGCTTTAGCTATTTTTGCTCTTTTAAACGTAAATAATATGTTAAATTCAGAAACTTCTCAAATTTTAACCGCGGTTGTAATTATATCTATGGTAGCTACTCCGTTTATATTAAAAAACATCGGACATTTAGCCGACAGACTAGAAGAAGAGAGCGAAATACCTGAGTT
>S-907-1_CampylobacterfetusMLST-glyA_consensus
CCGAGTTTTTTAGCGTTTGTCTTTACTTGCTTAGCATAAACTTTCCACTCGTCACTAAGATTATGCTTAAATCCAACTGCTTTTCCAGCAATCACGTGCATAAGCGGCCCGCCTTGAATTCCCGGAAATATAGAACTATTTATTTTTTTAGCAAATTCCTCATCATTTGTCATGATGATACCGCCTCTTGGACCTCTTAATGTTTTATGAGTAGTTGAACTTACAACGTGACAGTGAGGAAATGGATTGTTATGTTCTCCTGCTACTACAAGACCTGCTATATGAGCAACATCGGCAAATAAATATGCTCCAACGCTATCGGCTATCTCTCTAAATTTCTTAAAATCAATCTCTCTAGCATAAGCACTAGCACCGCAAACTATCATTTTAGGTTTAGTTATATTTGCTATCTCTTCTACTTTATTATAATTTATACGTCCATCAAGCTCAACACCGTAGAAAAAGCTCTCATAGTTTTTTCCAGAGCTTGAAACTTTAGAACCGTGAGTAAGGTGTCCACCATGGCTTA
>S-907-1_CampylobacterfetusMLST-uncA_consensus
GAACTGAGCAAAAGCTTGAAGTTCGCGATACTGAGCAAGATCAAGCCTTAGTGTTCCAGAAACTTTTTTGATAGCTTTTATCTGGGCTGATCCGCCGACACGACTAACAGACAAACCAACGTTAATAGCAGGACGAATACCTGAGTTAAACAAGTCGCTTTCCAAGAAAATTTGACCATCAGTTATAGAAATAACATTTGTAGGAATATACGCTGAAACGTCACCTGCTTGAGTCTCGATAATAGGTAGAGCCGTAAGACTTCCCGCTCCTAGTTTATCACTTAGCTTACTAGCTCTCTCAAGCAGTCTTGAGTGCAGATAGAAAACATCTCCTGGATATGCTTCACGACCCGGCGGTCTTCTTAAAATCAATGACATTTCACGGTAAGCTACAGCGTGCTTGCTTAGATCATCATAAATAATAAGAGCATGGCGTGAGTTATCACGGAAATATTCACCCATTGTTACACCTCCATATGGAGCAAGATATTGTAACGCCGGAGCATCGCTTGCACTTGCATTAACTACTATAGTATA
Download FASTA file